Hmdb loader

Showing metabocard for Piperazine (HMDB0014730)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
enzymes (2) Show 2 proteins
Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2023-02-21 17:18:15 UTC
HMDB IDHMDB0014730
Secondary Accession Numbers
  • HMDB14730
Metabolite Identification
Common NamePiperazine
DescriptionPiperazine is an organic compound that consists of a six-membered ring containing two opposing nitrogen atoms. Piperazine exists as small alkaline deliquescent crystals with a saline taste. Piperazine was introduced to medicine as a solvent for uric acid. When taken into the body the drug is partly oxidized and partly eliminated unchanged. Outside the body, piperazine has a remarkable power to dissolve uric acid and producing a soluble urate, but in clinical experience it has not proved equally successful. Piperazine was first introduced as an anthelmintic in 1953. A large number of piperazine compounds have anthelmintic action. Their mode of action is generally by paralysing parasites, which allows the host body to easily remove or expel the invading organism.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0014730 (Piperazine)

592
  Mrv0541 02231214482D          

  6  6  0  0  0  0            999 V2000
    2.3645   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0014730 (Piperazine)

HMDB0014730
     RDKit          3D
Piperazine
 16 16  0  0  0  0  0  0  0  0999 V2000
    1.1443   -0.7085    0.3569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0360   -1.3439   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2436   -0.6474    0.0995 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1112    0.7154   -0.4428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0282    1.3702    0.4134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2155    0.6975    0.0309 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0524   -1.2000   -0.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0015   -0.8538    1.4423 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0191   -1.2878   -1.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0730   -2.4099   -0.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1840   -0.5569    1.1317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0757    1.2092   -0.3606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7637    0.6519   -1.5041 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0749    2.4438    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2592    1.1504    1.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2669    0.7699   -1.0193 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
M  END
Download

3D SDF for HMDB0014730 (Piperazine)

592
  Mrv0541 02231214482D          

  6  6  0  0  0  0            999 V2000
    2.3645   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014730

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CNCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2

> <INCHI_KEY>
GLUUGHFHXGJENI-UHFFFAOYSA-N

> <FORMULA>
C4H10N2

> <MOLECULAR_WEIGHT>
86.1356

> <EXACT_MASS>
86.08439833

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
9.973273418817676

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
piperazine

> <ALOGPS_LOGP>
-1.16

> <JCHEM_LOGP>
-0.72880683

> <ALOGPS_LOGS>
0.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.559244671699773

> <JCHEM_POLAR_SURFACE_AREA>
24.06

> <JCHEM_REFRACTIVITY>
25.4488

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.71e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
piperazine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0014730 (Piperazine)

HMDB0014730
     RDKit          3D
Piperazine
 16 16  0  0  0  0  0  0  0  0999 V2000
    1.1443   -0.7085    0.3569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0360   -1.3439   -0.3412 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2436   -0.6474    0.0995 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1112    0.7154   -0.4428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0282    1.3702    0.4134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2155    0.6975    0.0309 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0524   -1.2000   -0.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0015   -0.8538    1.4423 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0191   -1.2878   -1.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0730   -2.4099   -0.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1840   -0.5569    1.1317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0757    1.2092   -0.3606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7637    0.6519   -1.5041 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0749    2.4438    0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2592    1.1504    1.4884 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2669    0.7699   -1.0193 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
M  END
Download

PDB for HMDB0014730 (Piperazine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 592                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  N   UNK     0       4.414  -1.540   0.000  0.00  0.00           N+0
HETATM    2  N   UNK     0       4.414   1.540   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       5.748  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.080  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.748   0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.080   0.770   0.000  0.00  0.00           C+0
CONECT    1    3    4                                                       
CONECT    2    5    6                                                       
CONECT    3    1    5                                                       
CONECT    4    1    6                                                       
CONECT    5    2    3                                                       
CONECT    6    2    4                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
Download

3D PDB for HMDB0014730 (Piperazine)

COMPND    HMDB0014730
HETATM    1  C1  UNL     1       1.144  -0.708   0.357  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.036  -1.344  -0.341  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.244  -0.647   0.100  1.00  0.00           N  
HETATM    4  C3  UNL     1      -1.111   0.715  -0.443  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.028   1.370   0.413  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.215   0.697   0.031  1.00  0.00           N  
HETATM    7  H1  UNL     1       2.052  -1.200  -0.041  1.00  0.00           H  
HETATM    8  H2  UNL     1       1.002  -0.854   1.442  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.019  -1.288  -1.437  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.073  -2.410  -0.026  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.184  -0.557   1.132  1.00  0.00           H  
HETATM   12  H6  UNL     1      -2.076   1.209  -0.361  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.764   0.652  -1.504  1.00  0.00           H  
HETATM   14  H8  UNL     1       0.075   2.444   0.208  1.00  0.00           H  
HETATM   15  H9  UNL     1      -0.259   1.150   1.488  1.00  0.00           H  
HETATM   16  H10 UNL     1       1.267   0.770  -1.019  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    9   10
CONECT    3    4   11
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6   16
END
Download

SMILES for HMDB0014730 (Piperazine)

C1CNCCN1
Download

INCHI for HMDB0014730 (Piperazine)

InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC4H10N2
Average Molecular Weight86.1356
Monoisotopic Molecular Weight86.08439833
IUPAC Namepiperazine
Traditional Namepiperazine
CAS Registry Number110-85-0
SMILES
C1CNCCN1
InChI Identifier
InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2
InChI KeyGLUUGHFHXGJENI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperazines. Piperazines are compounds containing a piperazine ring, which is a saturated aliphatic six-member heterocyclic with two nitrogen atoms at positions 1 and 4, as well as four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazinanes
Sub ClassPiperazines
Direct ParentPiperazines
Alternative Parents
Substituents
  • Piperazine
  • Azacycle
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point106 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility371 g/LNot Available
LogP-0.8Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00592 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00592 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00592
Phenol Explorer Compound IDNot Available
FooDB IDFDB012189
KNApSAcK IDNot Available
Chemspider ID13835459
KEGG Compound IDC07973
BioCyc IDPIPERAZINE
BiGG IDNot Available
Wikipedia LinkPiperazine
METLIN IDNot Available
PubChem Compound4837
PDB IDPZE
ChEBI ID28568
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Cytochrome P450 2D6
General function:
Involved in monooxygenase activity
Specific function:
Responsible for the metabolism of many drugs and environmental chemicals that it oxidizes. It is involved in the metabolism of drugs such as antiarrhythmics, adrenoceptor antagonists, and tricyclic antidepressants.
Gene Name:
CYP2D6
Uniprot ID:
P10635
Molecular weight:
55768.94
References
  1. Preissner S, Kroll K, Dunkel M, Senger C, Goldsobel G, Kuzman D, Guenther S, Winnenburg R, Schroeder M, Preissner R: SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions. Nucleic Acids Res. 2010 Jan;38(Database issue):D237-43. doi: 10.1093/nar/gkp970. Epub 2009 Nov 24. [PubMed:19934256 ]
Enzyme Details
2. Gamma-aminobutyric acid receptor subunit beta-3
General function:
Involved in ion transport
Specific function:
GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel
Gene Name:
GABRB3
Uniprot ID:
P28472
Molecular weight:
54115.0
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Maskell PD, Wafford KA, Bermudez I: Effects of gamma-HCH and delta-HCH on human recombinant GABA(A) receptors: dependence on GABA(A) receptor subunit combination. Br J Pharmacol. 2001 Jan;132(1):205-12. [PubMed:11156579 ]
  4. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]